Peer-reviewed journal papers (n=52) by research areas
Peer-reviewed
Research Articles
2020
- Chen X, Li D*. Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data. Genomics. 2020 Dec 7. doi: 10.1016/j.ygeno.2020.12.004. Online ahead of print. PMID: 33301893. (* corresponding author). (This study identified viral reads in human blood whole-genome
sequencing datasets and distinguished true viral reads from reads
associated with technical variables such as sequencing platform and DNA
source. The results will help improve the filtering of sequencing reads in
future (meta)genomic studies.)
- Sulovari A, Li D*.
VIpower: Simulation-based tool for estimating power of viral integration
detection via high-throughput sequencing. Genomics.
2020 Jan 10;112(1):207-211.
PMID: 30710609. (* corresponding
author). (This study helps
design new sequencing experiments to increase the power and accuracy to
detect genome-wide viral integrations, including ERVs and other transposable
elements.)
- Nepotchatykh E, Elremaly W, Caraus I, Godbout C, Leveau C, Chalder
L, Beaudin C, Kanamaru E, Kosovskaia R, Lauzon S, Maillet Y, Franco A,
Lascau-Coman V, Bouhanik S, Gaitan YP, Li D, Moreau A. Profile
of circulating microRNAs in myalgic encephalomyelitis and their relation
to symptom severity, and disease pathophysiology. Scientific Reports. 2020
Nov 12;10(1):19620. PMID: 33184353.
2019
- Chen X, Kost J, Sulovari A, Wong N, Liang WS, Cao J, Li D*. A virome-wide clonal
integration analysis platform for discovering cancer viral etiology. Genome
Research.
2019 May;29(5):819-830.
PMID: 30872350. (* corresponding
author). (A high-throughput sequencing-based
bioinformatics approach to detection of viral integration events in the
human genome on the virome-wide level, named VIcaller, was developed and
demonstrated in genome datasets.)
- Chen X, Li D*.
ERVcaller: Identifying polymorphic endogenous retrovirus and other
transposable element insertions using whole-genome sequencing data. Bioinformatics.
2019 Oct 15;35(20):3913-3922. PMID: 30895294. (* corresponding author). (A
high-throughput sequencing-based bioinformatics approach to genome-wide
genotyping of ERVs and other TEs, named ERVcaller, was developed. This
tool allows for genome-wide association studies of TEs with any complex
disease.)
- Chen X, Kost J, Li D*.
Comprehensive comparative analysis of methods and software for identifying
viral integrations. Briefings in Bioinformatics. 2019 Nov 27;20(6):2088-2097. PMID:
30102374. (* corresponding
author). (This
study, for the first time, proposed the “virome-wide” concept for viral
integration detection.)
- Nada D, Julien C, Rompré PH, Akoume MY, Gorman KF, Samuels ME,
Levy E, Kost J, Li D,
Moreau A. Association of Circulating YKL-40 Levels and CHI3L1 Variants
with the Risk of Spinal Deformity Progression in Adolescent Idiopathic
Scoliosis. Scientific Reports. 2019 Apr 5;9(1):5712. PMID: 30952886.
2018
- Sulovari A, Liu Z, Zhu Z*, Li
D*. Genome-wide meta-analysis of copy number variations with
alcohol dependence. Pharmacogenomics Journal. 2018
May 22;18(3):398-405. PMID: 28696413. (* corresponding author). (First genome-wide
meta-analysis of CNVs in any substance abuse)
- Zhao FQ, Misra Y, Li DB, Wadsworth MP, Krag D, Weaver D, Tessitore
J, Li DW, Zhang G, Tian
Q, Buss K. Differential expression of Oct3/4 in human breast cancer and
normal tissues. International Journal of Oncology. 2018 Jun;52(6):2069-2078. PMID:
29620155.
2017
- Sulovari A, Chen YH, Hudziak JJ, Li D*. Atlas of human diseases influenced by genetic
variants with extreme allele frequency differences. Human Genetics. 2017 Jan;136(1):39-54.
PMID: 27699474.
(* corresponding author). (This study found that variants with large allele frequency variations
were associated with a wide range of human complex diseases)
2015
- Li D*, Zhao H, Kranzler HR, Li M, Jensen KP,
Zayats T, Farrer LA, Gelernter J. Genome-wide Association Study of Copy
Number Variations (CNVs) With Opioid Dependence. Neuropsychopharmacology.
2015 Mar;40(4):1016-26. PMID: 25345593. PMCID: PMC4330517. (* corresponding author) (First
genome-wide CNV study in any drug dependence)
- Sulovari A, Kranzler HR, Farrer LA, Gelernter J, Li D*. Eye Color: A
Potential Indicator of Alcohol Dependence Risk in European Americans. American
Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2015 Jul;168(5):347-53. PMID:
25921801. (* corresponding
author). (Featured in Huffington Post, ABC news,
CBS News, WPTZ-TV, and other media reports in July 2015)
2014
- Sulovari A, Li D*.
GACT: a Genome build and Allele definition Conversion Tool for SNP
imputation and meta-analysis in genetic association studies. BMC
Genomics. 2014 Jul 19;15(1):610. PMID: 25038819. (* corresponding author)
- Li D*, Sulovari A, Cheng C, Zhao H, Kranzler
HR, Gelernter J. Association of Gamma-Aminobutyric Acid A Receptor α 2
Gene (GABRA2) with Alcohol Use Disorder. Neuropsychopharmacology.
2014 Mar;39(4):907-18. PMID: 24136292. PMCID: PMC3924525.
(* corresponding author) (NIH Relative Citation Ratio = 3.90; NIH
Percentile = 90.3). (First
meta-analysis of drug dependence with GABA receptor genes)
- Cao J, Liu X, Han S, Zhang CK, Liu Z, Li D*. Association of the HTR2A gene with alcohol and
heroin abuse. Human Genetics.
2014 Mar;133(3):357-65. PMID: 24178752. PMCID: PMC4085799. (* corresponding author)
- Yang H, Li D,
Cheng C. Relating gene expression evolution with CpG content changes. BMC
Genomics. 2014 Aug 20;15(1):693. PMID: 25142157. PMCID:
PMC4148958.
2013
- Cao J, Hudziak J, Li D*.
Multi-cultural Association of the Serotonin Transporter Gene (SLC6A4) with
Substance Use Disorder. Neuropsychopharmacology. 2013
Aug;38(9):1737-47. PMID: 23518607. PMCID: PMC3717550. (* corresponding author)
- Cao J, LaRocque E, Li D*. Associations of the
5-hydroxytryptamine (Serotonin) Receptor 1B Gene (HTR1B) with Alcohol,
Cocaine, and Heroin Abuse. American Journal of Medical Genetics
Part B: Neuropsychiatric Genetics. 2013 Mar;162(2):169-76. PMID: 23335468. PMCID: PMC4089973.
(* corresponding author)
- Wang L, Jiao Y, Huang Y, Liu X, Gibson G, Bennett B, Hamre KM, Li D, Zhao H, Gelernter J,
Kranzler HR, Farrer LA, Lu L, Wang Y, Gu W. Critical evaluation of
transcription factor Atf2 as a candidate modulator of alcohol preference
in mouse and human populations. Genetics and Molecular Research. 2013 Nov 26;12(4):5992-6005.
PMID: 24338393.
2012
- Li D, Zhao H, Kranzler HR, Oslin D, Anton
RF, Farrer LA, Gelernter J. Association of COL25A1 with comorbid
antisocial personality disorder and substance dependence. Biological
Psychiatry. 2012 Apr 15;71(8):733-40. PMID: 22297151. PMCID:
PMC3548659. (First
genome-wide association study of this disorder; another study showed
COL25A1 was a driver gene for behavioral alteration in mice.)
- Li D*, Zhao H, Gelernter J. Further
clarification of the contribution of the ADH1C gene to vulnerability of
alcoholism and selected liver diseases. Human Genetics. 2012
Aug;131(8):1361-74. PMID: 22476623. PMCID: PMC3557796. (* corresponding author)
- Li D*, Zhao H, Gelernter J. Strong protective
effect of the aldehyde dehydrogenase gene (ALDH2) 504lys (*2) allele
against alcoholism and alcohol-induced medical diseases in Asians. Human
Genetics. 2012 May;131(5):725-37. PMID: 22102315. PMCID:
PMC3548401. (* corresponding author) (120 citations) (NIH Relative Citation Ratio = 2.70; NIH
Percentile = 83.1)
- Zhang H, Li D,
Su Y, Jiang S, Xu Y, Jiang K, Cui D. Identification of the
N-acylsphingosine amidohydrolase 1 gene (ASAH1) for susceptibility to
schizophrenia in a Han Chinese population. World Journal Biological
Psychiatry. 2012 Feb;13(2):106-13. PMID: 21375364.
2011
- Li D*, Zhao H, Gelernter J.
Strong association of the alcohol dehydrogenase 1B gene (ADH1B) with
alcohol dependence and alcohol-induced medical diseases. Biological
Psychiatry. 2011 Sep 15;70(6):504-12. PMID: 21497796. PMCID:
PMC3142297. (*
corresponding author) (130
citations; NIH Relative Citation Ratio = 3.71; NIH Percentile = 89.5)
- Cui D, Zhang H, Yang BZ, Listman JB, Li D, Price LH, Carpenter
LL, Tyrka AR, Anton RF, Kranzler HR, Gelernter J. Variation in NGFB is
associated with primary affective disorders in women. American Journal of Medical
Genetics Part B: Neuropsychiatric Genetics. 2011
Jun;156B(4):401-12. PMID: 21294249. PMCID: PMC3108453.
2010
- Bertisch
H, Li D, Hoptman MJ,
Delisi LE. Heritability estimates for cognitive factors and brain white
matter integrity as markers of schizophrenia. American Journal of Medical
Genetics Part B: Neuropsychiatric Genetics. 2010 Jun
5;153B(4):885-94. PMID: 20052692. PMCID: PMC3446203.
- Proudnikov D, Kroslak T, Sipe JC, Randesi M, Li D, Hamon S, Ho A, Ott J,
Kreek MJ. Association of polymorphisms of the cannabinoid receptor (CNR1)
and fatty acid amide hydrolase (FAAH) genes with heroin addiction: impact
of long repeats of CNR1. Pharmacogenomics Journal. 2010 Jun;10(3):232-42. PMID: 20010914.
- Hilner JE, Perdue LH, Sides EG, Pierce JJ, Wägner AM,
Aldrich A, Loth A, Albret L, Wagenknecht LE, Nierras C, Akolkar B; Type 1
Diabetes Genetics Consortium. Designing and implementing sample and data collection
for an international genetics study: the Type 1 Diabetes Genetics
Consortium (T1DGC). Clinical Trials. 2010;7(1
Suppl):S5-S32. PMID: 20603248.
2009
- Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper
JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot
F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS; Type
1 Diabetes Genetics Consortium. Genome-wide association study and
meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature
Genetics. 2009 Jun;41(6):703-7. PMID: 19430480. PMCID: PMC2889014.
- Li D*, Feng G, He L*.
Case-control study of association between the functional candidate gene
ERBB3 and schizophrenia in Caucasian population. World Journal of Biological Psychiatry. 2009;10(4 Pt 2):595-8.
PMID: 19995212. (*
co-corresponding author)
- Li D*, He G, Xu Y, Duan Y, Gu N,
Li X, Shi Y, Qin W, Feng G, He L. Schizophrenia is not associated with the
ERBB3 gene in a Han Chinese population sample: Results from case-control
and family-based studies. Genetics and Molecular Biology.
2009 Oct;32(4):729-30. PMID: 21637446. PMCID: PMC3036886. (* co-corresponding
author)
- He C, Hamon S, Li D, Barral S, Ott J.
MHC fine mapping of human type 1 diabetes using the T1DGC data. Diabetes, Obesity and Metabolism.
Vol 11, Suppl 1, 2009 Jan, 53-9. PMID: 19143815. PMCID: PMC2753855.
2008
- Li D*, He L*. Meta-study on association between the monoamine
oxidase A gene (MAOA) and schizophrenia. American Journal of Medical
Genetics Part B: Neuropsychiatric Genetics. 2008 Mar
5;147B(2):174-8. PMID: 17894408. (*
co-corresponding author)
- Levran O, O'Hara K, Peles E, Li D, Barral S, Ray B, Borg L, Ott J, Adelson M, Kreek
MJ. ABCB1 (MDR1) genetic variants are associated with methadone doses
required for effective treatment of heroin dependence. Human
Molecular Genetics. 2008 Jul 15;17(14):2219-27. PMID: 18424454.
PMCID: PMC2599947. (157 citations; NIH
Relative Citation Ratio = 3.45; NIH Percentile = 88.2)
2007
- Li D, He L. Meta-analysis supports association between serotonin
transporter (5-HTT) and suicidal behavior. Molecular Psychiatry. 2007 Jan;12(1):47-54. PMID: 16969368. (208 citations)
- Li D*, He L*. Association study between the NMDA receptor 2B
subunit gene (GRIN2B) and schizophrenia: a HuGE review and meta-analysis. Genetics in Medicine. 2007 Jan;9(1):4-8. PMID: 17224684. (*co-corresponding author)
- Li D*, He L. G72/G30
genes and schizophrenia: a systematic meta-analysis of association
studies. Genetics. 2007
Feb;175(2):917-22. PMID: 17179078. PMCID: PMC1800627. (* corresponding author)
- Li D*, He L*. Association study between the dystrobrevin binding
protein 1 gene (DTNBP1) and schizophrenia: a meta-analysis. Schizophrenia Research. 2007
Nov;96(1-3):112-8. PMID: 17604607. (*co-corresponding author)
2006
- Li D, Sham PC, Owen MJ, He L. Meta-analysis shows significant
association between dopamine system genes and attention deficit
hyperactivity disorder (ADHD). Human Molecular Genetics. 2006
Jul 15;15(14):2276-84. PMID: 16774975. (668 citations; NIH Relative Citation Ratio = 10.13; NIH Percentile
= 98.3)
- Li D, Collier DA, He L. Meta-analysis shows strong positive
association of the neuregulin 1 (NRG1) gene with schizophrenia. Human Molecular Genetics.
2006 Jun 15;15(12):1995-2002.
PMID: 16687441. (351
citations; NIH Relative Citation Ratio = 6.12; NIH Percentile = 95.5)
- Li D, He L. Further clarification of the contribution of the tryptophan
hydroxylase (TPH) gene to suicidal behavior using systematic allelic and
genotypic meta-analyses. Human Genetics.
2006 Apr;119(3):233-40. PMID:
16450114. (126
citations)
- Li D,
He L. Meta-analysis shows association between the tryptophan hydroxylase
(TPH) gene and schizophrenia. Human Genetics. 2006
Aug;120(1):22-30. PMID: 16741719.
- Li D,
He L. Association study of the G-protein signaling 4 (RGS4) and proline
dehydrogenase (PRODH) genes with schizophrenia: a meta-analysis. European Journal of Human Genetics.
2006 Oct;14(10):1130-5. PMID: 16791139.
- Li D, Duan Y, He L. Association study of serotonin 2A receptor
(5-HT2A) gene with schizophrenia and suicidal behavior using systematic
meta-analysis. Biochemical and
Biophysical Research Communications. 2006 Feb 17;340(3):1006-15. PMID: 16405867. (122 citations)
- Zhang X, Li D, Duan
S, Duan Y, Chen Q, Li X, Liu Z, Feng G, He L. Analysis of the association
between Apolipoprotein D and schizophrenia. Neuropsychobiology. 2006Nov;54(1):40-4. PMID:
16966838.
- Liu X, Li H, Qin W, He G, Li D, Shen Y,
Shen J, Gu N, Feng G, He L. Association of TPH1 with suicidal behaviour
and psychiatric disorders in the Chinese population. Journal of Medical Genetics. 2006 Feb;43(2):e4. PMID:
16467214. PMCID: PMC2564644.
2005
- Pan Y, Li
D, Duan Y, Zhang Z, Xu M, Feng G, He L. Predicting protein
subcellular location using digital signal processing. Acta Biochimica et Biophysica Sinica. 2005 Feb;37(2):88-96. PMID:
15685365.
- Liu X,
Qin W, He G, Yang Y, Chen Q, Zhou J, Li D, Gu N, Xu Y, Feng
G, Sang H, Hao X, Zhang K, Wang S, He L. A family-based association study
of the MOG gene with schizophrenia in the Chinese population. Schizophrenia Research.
2005 Mar 1;73(2-3):275-80. PMID: 15653272.
- Liu J,
Shi Y, Tang W, Guo T, Li D, Yang Y, Yang Y, Zhao X, Wang H,
Li X, Feng G, Gu N, Zhu S, Liu H, Guo Y, Shi J, Sang H, Yan L, He L.
Positive association of the human GABA-A-receptor beta 2 subunit gene
haplotype with schizophrenia in the Chinese Han population. Biochemical and Biophysical Research Communications. 2005 Sep 2;334(3):817-23. PMID: 16023997.
2004
- Li D, Pan Y, Duan Y, Hung
Z, Xu M, He L. Understanding SARS with Wolfram approach. Acta Biochimica et Biophysica
Sinica. 2004
Jan;36(1):1-10. PMID: 14732867.
- Liu X, He
G, Wang X, Chen Q, Qian X, Lin W, Li D, Gu N, Feng G, He L.
Association of DAAO with schizophrenia in the Chinese population. Neuroscience Letters. 2004
Oct 21;369(3):228-33. PMID: 15464270.
- Yang Y,
Xiao Z, Chen W, Sang H, Guan Y, Peng Y, Zhang D, Gu Z, Qian M, He G, Qin
W, Li D, Gu N, He L. Tumor suppressor gene TP53 is
genetically associated with schizophrenia in the Chinese population. Neuroscience Letters. 2004
Oct 14;369(2):126-31. PMID: 15450681.
Peer-reviewed Review Articles
2018
- Cao* J, Li D*. Searching
for human oncoviruses: histories, challenges, and opportunities. Journal of Cellular Biochemistry. 2018 Jun;119(6):4897-4906.
PMID: 29377246. (* corresponding
author). (This study, for the first time,
proposed the “clonal integration analysis” concept.)
Non-Peer
Reviewed Journal Publications
Letters to editor
- Sulovari A, Kranzler HR, Farrer LA, Gelernter J, Li D*. Further analyses
support the association between light eye color and alcohol dependence. American Journal of Medical
Genetics Part B: Neuropsychiatric
Genetics. 2015 Dec;168(8):757-60. PMID: 26290254. (* corresponding author).
- Han S, Ma L, Li
D, Yang BZ. Is the tail-strength measure more powerful in tests of
genetic association? American Journal of Human Genetics. 2009 Feb;84(2):295-8. PMID: 19215734. PMCID:
PMC2668021.
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